Currently accessible and affordable high-throughput sequencing methods are best suited to the characterization of short-range sequence contiguity and genomic variation. Achieving long-range linkage and haplotype phasing requires either the ability to directly and accurately read long (e.g., tens of kilobases) sequences, or the capture of linkage and phase relationships through paired or grouped sequence reads. However, grouping sequencing information and generating an assembly of the sequence information necessary to achieve long-range linkage and haplotype phasing is computationally intensive and time consuming. Disclosed herein are computationally efficient methods and systems to obtain assemblies with chromosome-scale contiguity from sequence information informed by paired or grouped sequence reads.